sequence element (kmer) enrichment analysis
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README.md

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seer

Sequence element enrichment analysis. This document contains installation instuctions. Usage can be found on the wiki, and more information in the paper.

NOTE: seer has now been superseded by pyseer. We would recommend you use that implementation instead.

Usage, interpretation of results, and troubleshooting

See the wiki

Installation

These options are roughly listed in increasing order of difficulty. seer only works on Linux.

Use bioconda

Simply run:

conda install seer

If you do not have conda, first install miniconda then add the necessary channels:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

Use homebrew

If you have homebrew, the following recipe is available:

brew tap tseemann/homebrew-bioinformatics-linux
brew tap homebrew/science
brew install seer

Use a pre-compiled release

Head to the release page and download and unpack the tarball. If you have the dependencies installed use the dynamic version, otherwise use the static version (tested on Ubuntu only; static_all should work on other 64-bit Linux platforms).

Use on a virtual machine

We have a virtual machine, containing SEER and other useful bioinformatics programs, which is available at ftp://ftp.sanger.ac.uk/pub/pathogens/pathogens-vm/pathogens-vm.latest.ova and can be imported as an appliance in VirtualBox.

Compile source code

First clone the repository

git clone --recursive https://github.com/johnlees/seer

If you already have dlib:

git clone https://github.com/johnlees/seer

Currently tested on Linux only, installation should proceed as

make
make install

Full installation instructions are available below

Dependencies

seer currently depends on

You will also require

  • gcc >4.9 or equivalent
  • gcc libstdc++ >4.9

You probably already have boost, HDF5 and dlib (as long as you did clone --recursive).

Installation on Ubuntu/biolinux

Running the following commands will install seer

sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt-get update
sudo apt-get install g++-4.9 libhdf5-dev libopenblas-dev libboost-program-options-dev

git clone --recursive https://github.com/johnlees/seer
cd seer

wget http://www.cs.unc.edu/Research/compgeom/gzstream/gzstream.tgz
tar xzf gzstream.tgz
cd gzstream &&make CC=/usr/bin/gcc-4.9
cd ..

wget http://sourceforge.net/projects/arma/files/armadillo-6.700.6.tar.gz
tar xzf armadillo-6.700.6.tar.gz
cd armadillo-6.700.6
CXX=/usr/bin/g++-4.9 cmake .
make
sudo make install
sudo ldconfig /usr/lib64
cd ..
cd src && make CXX=/usr/bin/g++-4.9

If you are having trouble finding hdf5 (e.g. on Ubuntu 16.04) try running:

make CPPFLAGS="-I../gzstream -I../dlib -I/usr/include/hdf5/serial -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1"

General installation instructions

gzstream

Download and unpack to a folder gzstream in the root of the repository. Change into the directory and type

make

HDF5

Best installed with your distribution's package manager. Otherwise use a binary from https://www.hdfgroup.org/HDF5/release/obtain5.html, or if you wish to compile from source

gunzip < hdf5-X.Y.Z.tar.gz | tar xf -
cd hdf5-X.Y.Z
./configure --prefix=/usr/local/hdf5 <more configure_flags>
make
make check
make install
make check-install

armadillo

Make sure HDF5 is installed first.

Download and unpack. Change into directory and type

cmake -DARMA_USE_HDF5=1 .
make
make install

boost

Best installed with your distribution's package manager, and you should use the c++11 version if possible.

For a manual installation, see http://www.boost.org/doc/libs/1_57_0/more/getting_started/unix-variants.html for details on how to use ./b2 to install. I recommend that you create a user-config.jam file in the boost root which modifies the gcc compilation:

using gcc:
  : std11
  : g++
  : <cxxflags>-std=c++11

Then run

./bootstrap.sh
./b2 install toolset=gcc-std11

dlib

If not installed use the above git clone command to include with the repository. Otherwise unpack header files to $(PREFIX)/include

installation

Currently tested on Linux only, installation should proceed as

make
make install

You may need to explicitly set the current GCC compiler, which you can do by running

make CXX=g++-4.9